Abe sent the message to an annual ceremony held April 29 at the Koyasan temple in central Japan, but in his capacity as head of the ruling party, not as prime minister, Chief Cabinet Secretary Yoshihide Suga told reporters.
Suga was responding to a report by a Japanese newspaper that Abe's message, which was read out loud at the ceremony, said the war criminals had "sacrificed their souls to become the foundation of their country."
The revelation could worsen Japan's ties with China, which sees honouring war criminals as a lack of remorse by Tokyo aover wartime aggression.
The ceremony was held in front of a stone monument that honours about 1,180 Japanese war criminals, including wartime Prime Minister Hideki Tojo and 13 other executed leaders from the era.
The 14 "Class A" criminals, who are also honoured at Tokyo's Yasukuni Shrine, were convicted of crimes against peace and humanity by the International Military Tribunal for the Far East, held in Tokyo by the allied forces after the war.
Abe, however, has said that those convicted by the tribunal are not considered war criminals under domestic law.
Ceremony organisers said on their website that those who were executed were "wrongfully convicted" by the allies and that their honour should be restored.
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